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Molecular Insight into the Mutual Interactions of Two Transmembrane Domains of Human Glycine Receptor (TM23-GlyR), with the Lipid Bilayers 人甘氨酸受体(TM23-GlyR)两个跨膜结构域与脂质双层相互作用的分子观察
IF 1.2 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2020-09-01 DOI: 10.22036/PCR.2020.213221.1712
F. Hamedi, D. Mohammad-Aghaie
Appearing as a computational microscope, MD simulation can ‘zoom in’ to atomic resolution to assess detailed interactions of a membrane protein with its surrounding lipids, which play important roles in the stability and function of such proteins. This study has employed the molecular dynamics (MD) simulations, to determine the effect of added DMPC or DMTAP molecules on the structure of DPPC bilayer, and also to characterize the mutual interactions of TM23-GlyR (The second and third transmembrane domains of glycine receptor), with the pure and mixed lipid bilayers. Structural properties of DPPC bilayer, namely the order of acyl chains and the area per lipid, were affected by cationic DMTAP and zwitterionic DMPC lipids, in completely reverse ways. In the case of the mutual interactions of lipid molecules and TM23-GlyR, the cationic DMTAP lipids showed greater impact on the structural properties of this protein. On the other hand, TM23-GlyR caused clear increase in the lipid chain order, due to the positive hydrophobic mismatch. In total, this study could shed light on the effect of lipid force field, chain length, and the head group charge and size, on the lipid-protein interplay.
MD模拟看起来像一种计算显微镜,可以“放大”到原子分辨率,以评估膜蛋白与其周围脂质的详细相互作用,这些脂质在这些蛋白质的稳定性和功能中发挥着重要作用。本研究采用分子动力学(MD)模拟,确定添加DMPC或DMTAP分子对DPPC双层结构的影响,并表征TM23-GlyR(甘氨酸受体的第二和第三跨膜结构域)与纯脂质双层和混合脂质双层的相互作用。DPPC双层的结构性质,即酰基链的顺序和每脂的面积,受到阳离子DMTAP和两性离子DMPC脂质的影响,其方式完全相反。在脂质分子和TM23-GlyR相互作用的情况下,阳离子DMTAP脂质对该蛋白质的结构性质显示出更大的影响。另一方面,TM23-GlyR由于正疏水失配导致脂质链顺序明显增加。总之,这项研究可以阐明脂质力场、链长、头群电荷和大小对脂蛋白相互作用的影响。
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引用次数: 0
Quantum Chemical and Molecular Docking Studies of Imidazole and Its Derivatives as the Active Antifungal Components against C. Albicans 咪唑及其衍生物抗白念珠菌活性成分的量子化学和分子对接研究
IF 1.2 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2020-09-01 DOI: 10.22036/PCR.2020.211251.1706
S. Slassi, H. Zaki, A. Amine, K. Yamni, M. Bouachrine
Heterocyclic compounds based on Imidazole are very studied today because they are promising for pharmaceuticals applications and synthetic chemistry. Thus, the synthesis, characterization, and optical properties of four different Schiff bases ligands based on imidazole named L1-L4 has been reported by many authors. These compounds have been very studied especially their antifungal properties on an important fungal specie pathogenic for humans (Candida albicans). In this study, firstly the DFT quantum chemical calculations were performed on 4 structures based on Imidazole (L1, L2, L3 and L4) to determine their structural and electronic properties and to understand the correlation that exists between structure and their properties. In the second part, the molecular docking was carried out on the most and less active compounds (L1 and L4) with their targeted proteins to explain the origin of these in silico antioxidant properties and to examine the probable binding mode of the studied compounds with the corresponding amino acid residues of protein. The theoretical results were compared with experimental data.
以咪唑为基础的杂环化合物在药物应用和合成化学方面有着广阔的前景,因此目前研究较多。因此,许多作者报道了四种不同的基于咪唑的席夫碱配体L1-L4的合成、表征和光学性质。这些化合物已经得到了大量的研究,特别是它们对一种重要的人类致病真菌(白色念珠菌)的抗真菌特性。在本研究中,首先对咪唑的4个结构(L1、L2、L3和L4)进行了DFT量子化学计算,以确定它们的结构和电子性质,并了解结构与性质之间的相关性。在第二部分中,对活性最高和较低的化合物(L1和L4)及其靶蛋白进行了分子对接,以解释这些硅抗氧化特性的起源,并检查所研究的化合物与蛋白质相应氨基酸残基的可能结合模式。将理论结果与实验数据进行了比较。
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引用次数: 1
Selective Oxidation of Alkenes by Dioxygen Using Modified Gold Nanoclusters 改性金纳米团簇对烯烃的选择性氧化研究
IF 1.2 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2020-09-01 DOI: 10.22036/PCR.2020.220761.1735
H. Salari, M. Gholami
Selective oxidation of cyclohexene and styrene was investigated using molecular oxygen under mild conditions. Au/TiO2 and Au/Al2O3 surfaces were impregnated with three different ionic liquids. Supported ionic liquids (ILs) gold nanocatalysts are particularly versatile catalysts for oxidation reaction with exceptionally high efficiency and significant selectivity. Improved activity is attributed to the stabilization of reaction intermediates via different interaction such as hydrogen bonding and polarity/dipolarizability between ILs and intermediates. Surface coating of obtained nanoparticles with ionic liquids is found to increase the interaction energy. The estimated rate constant decreases in the following order: [EAP] > [bmim]PF6 > [emim]EtSO4. EAP/Au/Al2O3 exhibited maximum conversion compare to other IL-impregnated catalysts. Supported ionic liquids gold nanocatalysts are active catalysts for oxidation reaction with high efficiency and selectivity.
在温和条件下研究了分子氧对环己烯和苯乙烯的选择性氧化。用三种不同的离子液体浸渍Au/TiO2和Au/Al2O3表面。负载型离子液体(ILs)金纳米催化剂是一种特别通用的氧化反应催化剂,具有非常高的效率和显著的选择性。活性的提高是由于反应中间体通过不同的相互作用(如氢键和中间体之间的极性/偶极性)而稳定。结果表明,离子液体在纳米颗粒表面包覆可提高相互作用能。估算的速率常数递减顺序为:[EAP] > [bmim]PF6 > [emim]EtSO4。与其他il浸渍催化剂相比,EAP/Au/Al2O3的转化率最高。负载型离子液体金纳米催化剂是一种高效、选择性高的氧化反应活性催化剂。
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引用次数: 0
Functionalized Single-atom Thickness Boron Nitride Membrane for Separation of Arsenite Ion from Water: A Molecular Dynamics Simulation Study 功能化单原子厚度氮化硼膜分离水中亚砷离子的分子动力学模拟研究
IF 1.2 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2020-09-01 DOI: 10.22036/PCR.2020.222756.1742
Nasser Saadat Tabrizi, B. Vahid, J. Azamat
In this research, the performance of functionalized boron nitride nanosheet (BNNS) as a nanostructure membrane with single-atom thickness for the separation of arsenite ions from aqueous solution was examined by molecular dynamics simulation method. The simulated system included a functionalized BNNS placed in an ionic solution containing sodium arsenite, while the external pressures were applied to the system. For the high-water permeability and full ions rejection, the pore of BNNS was functionalized by passivizing pore edge atoms with F and H atoms. Then hydrostatic pressures in the range of 5-100 MPa was applied to the system. During the molecular dynamics simulations, water molecules and arsenite ions were monitored, and some analyses such as water flux, the density profile of water and ion, hydrogen bonds, and radial distribution function were obtained. Results showed that functionalized BNNS was able to conduct water molecules with high permeability through its pore, whereas ions were not able to pass through the pore.
本研究采用分子动力学模拟方法考察了功能化氮化硼纳米片(BNNS)作为单原子厚度纳米结构膜从水溶液中分离亚砷酸根离子的性能。模拟系统包括放置在含有亚砷酸钠的离子溶液中的功能化BNNS,同时对系统施加外部压力。由于BNNS具有高透水性和全离子排斥性,通过用F和H原子钝化孔边缘原子来对其孔进行功能化。然后将5-100MPa范围内的静水压力施加到系统上。在分子动力学模拟过程中,对水分子和亚砷酸根离子进行了监测,并获得了一些分析,如水通量、水和离子的密度分布、氢键和径向分布函数。结果表明,功能化的BNNS能够引导具有高渗透性的水分子通过其孔,而离子不能通过孔。
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引用次数: 4
First-order Nonlinear Optical Response of C2Bn-2H n-1X (n = 14-17; X = H, Li, Na, K, F, Cl, Br) Carboranes: Insights from DFT and TD-DFT Calculations C2Bn-2H n- 1x的一阶非线性光学响应(n = 14-17)X = H, Li, Na, K, F, Cl, Br)碳硼烷:来自DFT和TD-DFT计算的启示
IF 1.2 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2020-09-01 DOI: 10.22036/PCR.2020.224934.1749
Maryam Yousefizadeh, E. Shakerzadeh, M. Bamdad
Density functional theory (DFT) and time dependent density functional theory (TD-DFT) calculations were employed to investigate the electronic and nonlinear optical properties of some substituted C2Bn −2Hn (n = 14 −17) carboranes. Li, Na, K, F, Cl, Br are used as substituents. The carboranes substituted with alkali metal show considerably large first hyperpolarizability values than those of un-substituted ones. NLO response of the halogen-substituted systems is slightly enhanced. The well-known two-level model theory is investigated through TD-DFT approach to understand the origin of NLO response. This study indicates that alkali-metal substituted carboranes may be appropriate for nonlinear optical (NLO) applications.
采用密度泛函理论(DFT)和时间依赖密度泛函理论(TD-DFT)计算了一些取代的cbn - 2Hn (n = 14−17)碳硼烷的电子和非线性光学性质。Li, Na, K, F, Cl, Br被用作取代基。碱金属取代的碳硼烷比未取代的碳硼烷表现出相当大的第一超极化率。卤素取代体系的NLO响应略有增强。通过TD-DFT方法研究了著名的两级模型理论,以理解NLO响应的起源。该研究表明,碱金属取代碳硼烷可能适用于非线性光学应用。
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引用次数: 0
Investigation of Physicochemical Properties of Aggregated Models of [MIM+]2[C(CN)3-]2 Ionic Liquid: A Theoretical Study [MIM+]2[C(CN)3-]2离子液体聚集模型的物理化学性质研究
IF 1.2 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2020-06-01 DOI: 10.22036/PCR.2020.209284.1703
Batoul Maki̇abadi̇, M. Zakari̇anezhad
In present work, the aggregation behavior of ion-pairs in [MIM+]2[C(CN)3-]2 ionic liquid was investigated. The quantum chemical calculations were carried out to determine the structural parameters, interaction energies, hydrogen bonding, physical and topological properties of the clusters formed in the ionic liquid of [MIM+]2[C(CN)3-]2. The solvent effect on the stability of clusters was examined. The Gibbs free energy of solvation and the Gibbs free binding energy of clusters in various solvents were calculated. The results show that with decreasing the polarity of the solvent, the tendency to the formation of aggregate increases. Also, the solvation energies of the clusters increase with decreasing the solvent's dielectric constant. The NBO analysis was performed to evaluate the charge transfer in complexes. The AIM analysis was performed in order to characterize intermolecular interactions.
本文研究了离子对在[MIM+]2[C(CN)3-]2离子液体中的聚集行为。通过量子化学计算确定了[MIM+]2[C(CN)3-]2离子液体中形成的团簇的结构参数、相互作用能、氢键、物理和拓扑性质。考察了溶剂对团簇稳定性的影响。计算了不同溶剂中团簇的吉布斯自由能和吉布斯自由结合能。结果表明,随着溶剂极性的降低,聚合体的形成趋势增大。同时,随着溶剂介电常数的减小,团簇的溶剂化能增大。用NBO分析来评价配合物中的电荷转移。AIM分析是为了表征分子间相互作用。
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引用次数: 1
A Novel Poly(vinyl alcohol) Post-precipitation Template Synthesis and Property Tuning of Photoactive Mesoporous Nano-TiO2 新型聚乙烯醇沉淀后模板合成及光活性介孔纳米tio2性能调整
IF 1.2 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2020-06-01 DOI: 10.22036/PCR.2020.210668.1704
A. Hamisu, U. Gaya, A. Abdullah
For the first time, a facile method is introduced to obtain ultrathin, mesoporous TiO2 nanosheets by the alkali precipitation of aqueous TiCl3 in the presence of NH4OH, and in-situ templating with polyvinyl alcohol (PVA). The synthesized titania have been characterized by N2 adsorption-desorption measurements, x-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), thermo-gravimetric analysis (TGA) and ultraviolet-visible (UV-vis) spectroscopy. The obtained titania were hexagonal-like, detached, non-agglomerated, polydispersed, sub-20 nm nanodiscs. Unlike in doping methods, their surface area and pore volumes of can easily be tailored devoid of any wavelength shift, by simply tuning the amount of the template. Accordingly, their aggregation as microspheres can successfully be controlled by the templating step. The remarkable photoactivity of these nanoscopic materials has been confirmed by the degradation of aqueous methyl orange.
本文首次介绍了一种简单的方法,即在NH4OH存在下,将TiCl3水溶液碱沉淀,然后用聚乙烯醇(PVA)原位模板制备超薄介孔TiO2纳米片。通过氮气吸附-脱附、x射线衍射(XRD)、扫描电镜(SEM)、透射电镜(TEM)、热重分析(TGA)和紫外-可见光谱(UV-vis)对合成的二氧化钛进行了表征。所制得的二氧化钛呈六角形、离体、非团聚、多分散、亚20 nm纳米片状。与掺杂方法不同的是,通过简单地调整模板的量,可以很容易地在没有任何波长移动的情况下定制它们的表面积和孔体积。因此,通过模板步骤可以成功地控制它们作为微球的聚集。这些纳米材料具有显著的光活性,并通过降解甲基橙得到了证实。
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引用次数: 2
Separation of Acetic Acid from Water Using Organic Solvents: Liquid-Liquid Equilibrium Thermodynamic Investigation 用有机溶剂分离乙酸:液-液平衡热力学研究
IF 1.2 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2020-06-01 DOI: 10.22036/PCR.2020.205810.1693
Majid Mohadesi, R. Rezaei
Acetic acid is one of the most important carboxylic acids which is used in many reactions, including the synthesis of acetic esters. Because of industrial and environmental advantages, the separation of acetic acid from dilute aqueous solutions has recently received much attention. In this study we investigated liquid-liquid equilibrium of a ternary system consisted of water+ acetic acid+ organic solvent at various temperatures. In this study, various thermodynamic models (Non-Random Two-Liquid (NRTL) and Universal Quasi-Chemical (UNIQUAC) models) were used to predict the composition of component in aqueous and organic phases. In these models, intermolecular interaction were considered as a binomial function of reverse temperature. The parameters of two models were determined through the optimization of an objective function. Root mean square deviations of the NRTL and UNIQUAC models to predict the composition of the components in the ternary mixture of water+ acetic acid+ organic solvent were 0.0273 and 0.0422, respectively.
乙酸是最重要的羧酸之一,用于许多反应,包括乙酸酯的合成。由于工业和环境优势,从稀水溶液中分离乙酸最近受到了广泛关注。在本研究中,我们研究了由水+乙酸+有机溶剂组成的三元体系在不同温度下的液-液平衡。在本研究中,使用各种热力学模型(非随机双液(NRTL)和通用准化学(UNIQUAC)模型)来预测水相和有机相中组分的组成。在这些模型中,分子间相互作用被认为是反温度的二项式函数。两个模型的参数是通过优化目标函数来确定的。NRTL和UNIQUAC模型预测水+乙酸+有机溶剂三元混合物中组分组成的均方根偏差分别为0.0273和0.0422。
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引用次数: 2
Adsorption and Removal Characterization of Nitrobenzene by Graphene Oxide Coated by Polythiophene Nanoparticles 聚噻吩纳米颗粒包覆氧化石墨烯对硝基苯的吸附和去除表征
IF 1.2 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2020-06-01 DOI: 10.22036/PCR.2020.208780.1700
S. Mousavi, A. Babapoor, S. Hashemi, B. Medi
Nitrobenzene (NB) has a wide range of usages as a chemical intermediate and also as a dye in printing applications. Despite its advantages, NB is harmful to human and animals and hence is an environmental pollutant. In this research, NB removal from water was studied via adsorption on graphene oxide (GO) coated by polythiophene (PT) nanoparticles. The resulting nanocomposite was characterized by XRD, FTIR, BET, and SEM. While the FTIR tests proved successful incorporation of PT, the SEM images displayed a relatively larger surface area compared to other studies. The BET analysis confirms this finding by reporting the surface area as 917.8 m2/g for the adsorbent. The adsorption mechanism was assessed by the Langmuir and Freundlich isotherms. The results show that the Freundlich isotherm better describes the adsorption process compared to the Langmuir isotherm. On the other hand, the pseudo-second-order kinetic model better regresses the experimental results, which indicates a chemical adsorption mechanism. The adsorption-desorption behavior of the samples was evaluated at optimized pH, time, adsorbent dosage, and eluent type. The results showed that the synthesized nanocomposite can efficiently remove NB from solutions in the pH range of 5.0 to 7.0, with the maximum adsorption capacity of 15.6 mg/g.
硝基苯(NB)有广泛的用途,作为化学中间体,也作为染料在印刷应用。NB虽然有很多优点,但对人类和动物都是有害的,是一种环境污染物。在本研究中,研究了聚噻吩(PT)纳米颗粒包被氧化石墨烯(GO)吸附去除水中的NB。采用XRD、FTIR、BET和SEM对所制备的纳米复合材料进行了表征。虽然FTIR测试证明PT的成功结合,但与其他研究相比,SEM图像显示的表面积相对较大。BET分析通过报告吸附剂的表面积为917.8 m2/g证实了这一发现。采用Langmuir等温线和Freundlich等温线评价了吸附机理。结果表明,Freundlich等温线比Langmuir等温线更能描述吸附过程。另一方面,拟二级动力学模型较好地回归了实验结果,表明了化学吸附机理。在最佳的pH、时间、吸附剂用量和洗脱液类型下,对样品的吸附-解吸行为进行了评价。结果表明,合成的纳米复合材料在pH为5.0 ~ 7.0的溶液中均能有效去除NB,最大吸附量为15.6 mg/g。
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引用次数: 11
Nickel Hydrogenation Composite Catalysts Modified by Zirconium in Competitive Benzene Hydrogenation: Effect of Modifiers 锆改性苯竞争加氢镍加氢复合催化剂:改性剂的影响
IF 1.2 Q3 CHEMISTRY, MULTIDISCIPLINARY Pub Date : 2020-06-01 DOI: 10.22036/PCR.2020.206012.1694
N. Parsafard, M. H. Peyrovi, Mahdi Abdali Hajiabadi
A co-impregnation method was applied to the Ni/Zr-HMS/HZSM-5 catalyst (with various amounts of zirconium) during the hydrogenation of benzene. The physicochemical properties of the prepared nickel catalyst were characterized using X - ray diffraction, X - ray fluorescence, Fourier transform infrared spectroscopy, ultraviolet-visible diffuse reflectance spectroscopy, temperature-programmed desorption of ammonia, H2 chemisorption, N2 adsorption - desorption, and thermogravimetric analysis. The catalytic performance was assessed on a fixed-bed reactor (reaction temperature between 130 °C and 190 °C). The results indicated that the nickel catalyst with Si/Zr = 35 exhibited better catalytic performance and stability than others, so providing a better selectivity in long-term performance.
采用共浸渍法对不同锆用量的Ni/Zr-HMS/HZSM-5催化剂进行了苯加氢反应。采用X射线衍射、X射线荧光、傅里叶变换红外光谱、紫外-可见漫反射光谱、程序升温解吸氨、H2化学吸附、N2吸附-解吸、热重分析等方法对制备的镍催化剂的理化性质进行了表征。在固定床反应器(反应温度130 ~ 190℃)上评价了催化性能。结果表明,Si/Zr = 35的镍催化剂表现出较好的催化性能和稳定性,在长期性能上具有较好的选择性。
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引用次数: 1
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Physical Chemistry Research
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